Structure of PDB 9b8o Chain a Binding Site BS04

Receptor Information

>9b8o Chain a (length=422) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

TYNKTNKFTHGFQNIVDAYGIGTYREINPAPYTVITFPFLFAVMFGDFGH
GILMTLFAVWMVLRESRILSQKNENEMFSMVFSGRYIILLMGLFSIYTGL
IYNDCFSKSLNIFGSSWSVRPMFTIGNWTEETLLGSSVLQLNPAIPGVFG
GPYPFGIDPIWNIATNKLTFLNSFKMKMSVILGIIHMLFGVSLSLFNHIY
FKKPLNIYFGFIPEIIFMSSLFGYLVILIFYKWTAYDAHSSRNAPSLLIH
FINMFLFSYPESGNAMLYSGQKGIQCFLIVVAMLCVPWMLLFKPLILRHQ
YLRKKHVFDFGDTMVHQAIHTIEYCLGCISNTASYLRLWALSLAHAQLSE
VLWTMVIHIGLHVRSLAGGLGLFFIFAAFATLTVAILLIMEGLSAFLHAL
RLHWVEFQNKFYTGTGFKFLPF

Ligand information

Ligand ID

LP3

InChI

InChI=1S/C26H54NO7P/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-26(29)32-23-25(28)24-34-35(30,31)33-22-21-27(2,3)4/h25,28H,5-24H2,1-4H3/p+1/t25-/m1/s1

InChIKey

IHNKQIMGVNPMTC-RUZDIDTESA-O

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)O
ACDLabs 10.04	O=C(OCC(O)COP(=O)(OCC[N+](C)(C)C)O)CCCCCCCCCCCCCCCCC
CACTVS 3.341	CCCCCCCCCCCCCCCCCC(=O)OC[CH](O)CO[P](O)(=O)OCC[N+](C)(C)C
CACTVS 3.341	CCCCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](O)(=O)OCC[N+](C)(C)C
OpenEye OEToolkits 1.5.0	CCCCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OCC[N+](C)(C)C)O

Formula

C26 H55 N O7 P

Name

(7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE

PDB chain

9b8o Chain a Residue 903 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	9b8o High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles.
Resolution	3.2 Å
Binding residue (original residue number in PDB)	L415 C467 F468 S471 L472 N473 I474
Binding residue (residue number reindexed from 1)	L53 C105 F106 S109 L110 N111 I112
Annotation score	1

Gene Ontology

	Molecular Function
GO:0051117	ATPase binding

	Biological Process
GO:0007035	vacuolar acidification
GO:0008150	biological_process
GO:0016241	regulation of macroautophagy
GO:0097401	synaptic vesicle lumen acidification
GO:1902600	proton transmembrane transport

	Cellular Component
GO:0000220	vacuolar proton-transporting V-type ATPase, V0 domain
GO:0005737	cytoplasm
GO:0005886	plasma membrane
GO:0016020	membrane
GO:0016471	vacuolar proton-transporting V-type ATPase complex
GO:0030665	clathrin-coated vesicle membrane
GO:0030672	synaptic vesicle membrane
GO:0031410	cytoplasmic vesicle
GO:0042470	melanosome
GO:0043195	terminal bouton
GO:0045202	synapse
GO:0048471	perinuclear region of cytoplasm

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:9b8o, PDBe:9b8o, PDBj:9b8o
PDBsum	9b8o
PubMed	38900912
UniProt	P25286\|VPP1_RAT V-type proton ATPase 116 kDa subunit a 1 (Gene Name=Atp6v0a1)

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